Modelling ‘evo‐devo’ with RNA
Open accessAbstract
The folding of RNA sequences into secondary structures is a simple yet biophysically grounded model of a genotype–phenotype map. Its computational and mathematical analysis has uncovered a surprisingly rich statistical structure characterized by shape space covering, neutral networks and plastogenetic congruence. I review these concepts and discuss their evolutionary implications. BioEssays 24:1164–1177, 2002. © 2002 Wiley‐Periodicals, Inc.
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Different functions may await just a few mutations apart.
“Quoting Susanna Manrubia, these properties further ensure that different functions may await just a few mutations apart [46,49,50].”
From Fundamental constraints to the logic of living systems (2024) · cites this paper as [49]
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Bellman, R. E. (2010) · doi:10.1515/9781400835386 · Cited by 14,588 · see citing works
CANALIZATION OF DEVELOPMENT AND THE INHERITANCE OF ACQUIRED CHARACTERS
WADDINGTON, C. H. (1942) · Nature · doi:10.1038/150563a0 · Cited by 3,255 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
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Messina, C. D., Podlich, D., Dong, Z., Samples, M., & Cooper, M. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/erq329 · Cited by 233 · see citing works
The evolution of combinatorial gene regulation in fungi
Tuch, B. B., Galgoczy, D. J., Hernday, A. D., Li, H., & Johnson, A. D. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060038 · Cited by 228 · see citing works
Sloppiness, robustness, and evolvability in systems biology
Daniels, B. C., Chen, Y.-J., Sethna, J. P., Gutenkunst, R. N., & Myers, C. R. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.06.008 · Cited by 192 · see citing works
Modelling Crop Improvement in a G×E×M Framework via Gene–Trait–Phenotype Relationships
Messina, C., Hammer, G., Dong, Z., Podlich, D., & Cooper, M. (2009) · Crop Physiology · doi:10.1016/b978-0-12-374431-9.00010-4 · Cited by 121 · see citing works
Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., et al. (2021) · Physics of Life Reviews · doi:10.1016/j.plrev.2021.03.004 · Cited by 88 · see citing works
New structural variation in evolutionary searches of RNA neutral networks
Sumedha, Martin, O. C., & Wagner, A. (2007) · Biosystems · doi:10.1016/j.biosystems.2006.11.007 · Cited by 34 · see citing works
Fundamental constraints to the logic of living systems
Solé, R., Kempes, C. P., Corominas-Murtra, B., De Domenico, M., Kolchinsky, A., Lachmann, M., Libby, E., Saavedra, S., Smith, E., & Wolpert, D. (2024) · Interface Focus · doi:10.1098/rsfs.2024.0010 · Cited by 34 · see citing works
- Authors
- Fontana, W.
- Affiliations
- Santa Fe Institute (US)
- Corresponding author
- Fontana, Walter
- ORCID
- Fontana, Walter
- Venue
- BioEssays
- Publisher
- Wiley
- Published
- 2002-11-22
- Volume
- 24
- Issue
- 12
- Pages
- 1164-1177
- ISSN
- 0265-9247 (ISSN-L)
- 1521-1878
- OpenAlex
- W2102950230
- Cited by
- 179
- References
- 3
- Citations by year
- 2026: 6 · 2025: 2 · 2024: 2 · 2023: 6 · 2022: 7 · 2021: 4 · 2020: 5 · 2019: 5 · 2018: 6 · 2017: 4 · 2016: 6 · 2015: 7 · 2014: 8 · 2013: 4 · 2012: 14
- FWCI
- 0.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- BioEssays (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- John D. and Catherine T. MacArthur Foundation
- Santa Fe Institute
- National Institute on Aging (R01AG034994)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy and History of Science
- Keywords
- RNA secondary structure, genotype-phenotype mapping, evolutionary developmental biology, neutral networks, RNA folding, RNA evolution
- MeSH terms
- Algorithms, Genotype, Kinetics, Nucleic Acid Conformation, Phenotype, Phylogeny, RNA, Temperature, Thermodynamics, Time Factors, Neural Networks, Computer
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